Detection and phylogenetic analysis of contemporary H14N2 Avian influenza A virus in domestic ducks in Southeast Asia (Cambodia)

Abstract

Avian influenza virus (AIV) in Asia is a complex system with numerous subtypes and a highly porous wild birds-poultry interface. Certain AIV subtypes, such as H14, are underrepresented in current surveillance efforts, leaving gaps in our understanding of their ecology and evolution. The detection of rare subtype H14 in domestic ducks in Southeast Asia comprises a geographic region and domestic bird population previously unassociated with this subtype. These H14 viruses have a complex evolutionary history involving gene reassortment events. They share sequence similarity to AIVs endemic in Cambodian ducks, and Eurasian low pathogenicity and high pathogenicity H5Nx AIVs. The detection of these H14 viruses in Southeast Asian domestic poultry further advances our knowledge of the ecology and evolution of this subtype and reinforces the need for continued, longitudinal, active surveillance in domestic and wild birds. Additionally, in vivo and in vitro risk assessment should encompass rare AIV subtypes, as they have the potential to establish in poultry systems.

Keywords: H14N2; Southeast Asia; avian influenza; phylogenetics; surveillance.

Figure 1.

Location and characteristics of the duck farm in Cambodia. (A). Country map. Black lines denote provinces, and the capital Phnom Penh is indicated by a white circulate. Map was generated using QGIS (version 3.28.3). The duck farm from which H14 viruses were isolated is indicated in red. (B, C) Images of the semi free-ranging duck farm. Photographs were taken by Jurre Y. Siegers.

Figure 2.

Evolutionary relationships and divergence of HA gene of H14Nx viruses. Phylogeny includes all H14 HA sequences available in public influenza databases (GISAID, NCBI, and BV-BRC) with sequences generated in this study shown in red. Branches are coloured by geographic location. Tree is scaled to time with node bars corresponding to the 95% HPD. HA cleavage site motif is shown for each isolate.

Figure 3.

Phylogenetic relationship of the N2 gene sequences. Maximum Likelihood (ML) tree of Cambodian H14N2 viruses with HxN2 viruses. (A) Tree comprising all sequences in publicly available databases from 2018-2022. Red arrow indicates phylogenetic placement of Cambodian H14N2 in N2 tree for improved clarity. The tree was rooted to reflect geographic clades (B) comprising the >30 most closely related sequences. Sequences generated in this study are presented in red, with strain names emboldened. The tree was rooted against sequences from North America. Ultrafast bootstrap values (≥80) are presented. Scale bar indicates the number of nucleotide substitutions per site.

Figure 4.

Genome constellation of contemporary Cambodian H14N2 viruses. Genome constellation of each of the Cambodian H14N2 viruses, when available, are colour coded according to their genetic origin.